Identification and fine-mapping of a novel locus qSCL2.4 for resistance to Sclerotinia sclerotiorum in sunflower (Helianthus annuus)

Sclerotinia sclerotiorum (S. sclerotiorum) as a necrotrophic fungus severely threatens sunflower production. Despite abundant quantitative trait locus (QTL) for S. sclerotiorum resistance have been reported, the genetic and molecular basis remains largely unclear. Here, we performed QTL analysis for S. sclerotiorum resistance using a recombinant inbred line (RIL) population derived from resistant C6 and susceptible B728 parental lines. A high-density genetic linkage map of 17 linkage groups with 6,059 single nucleotide polymorphism (SNP) markers spanning 2,763 cM was constructed. Lesion length (LL) and lesion area (LA) were evaluated across field, climate chamber, and greenhouse trials using standardized inoculation protocols. Sixteen QTL for LL and twelve QTL for LA were identified with each QTL explaining 1.58 to 32.86% of the phenotypic variation. Of these, a major-effect QTL, qSCL2.4 on chromosome 2, explained up to 30.22% of phenotypic variance, which had allele conferring increased S. sclerotiorum resistance derived from the parent C6. Fine-mapping through a BC1F3 population derived from B728 × RIL-5 crosses narrowed the locus to a 226.7 kb interval. Functional annotation identified HaWRKY48 (LOC110907968), encoding a WRKY transcription factor, as the candidate gene. Seven nonsynonymous SNPs in HaWRKY48 distinguished resistant and susceptible alleles, with higher expression in B728 post-inoculation. A KASP marker targeting the causal SNP (Chr02:141503867) effectively discriminated haplotypes in 137 sunflower lines, with the favorable allele reducing lesion expansion by 40.06-48.92%. This study highlights qSCL2.4 as a pivotal locus for resistance and provides functional markers to accelerate breeding for sclerotinia-resistant sunflower cultivars.